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Lobster schema updates #924

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merged 4 commits into from
Jul 30, 2024
Merged

Lobster schema updates #924

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18da375
rename field name and adapt schema to work with latest monty release
naik-aakash Jul 20, 2024
9df77f3
apply ruff fixes
naik-aakash Jul 20, 2024
357055d
Merge branch 'materialsproject:main' into lobster_schema_updates
naik-aakash Jul 29, 2024
cf39a02
Merge branch 'materialsproject:main' into lobster_schema_updates
naik-aakash Jul 30, 2024
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82 changes: 46 additions & 36 deletions src/atomate2/lobster/schemas.py
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Original file line number Diff line number Diff line change
Expand Up @@ -323,12 +323,12 @@ def from_directory(
plot_kwargs = plot_kwargs or {}
lobsterpy_kwargs = lobsterpy_kwargs or {}
dir_name = Path(dir_name)
cohpcar_path = Path(zpath(dir_name / "COHPCAR.lobster"))
charge_path = Path(zpath(dir_name / "CHARGE.lobster"))
structure_path = Path(zpath(dir_name / "POSCAR"))
icohplist_path = Path(zpath(dir_name / "ICOHPLIST.lobster"))
icobilist_path = Path(zpath(dir_name / "ICOBILIST.lobster"))
icooplist_path = Path(zpath(dir_name / "ICOOPLIST.lobster"))
cohpcar_path = Path(zpath(str((dir_name / "COHPCAR.lobster").as_posix())))
charge_path = Path(zpath(str((dir_name / "CHARGE.lobster").as_posix())))
structure_path = Path(zpath(str((dir_name / "POSCAR").as_posix())))
icohplist_path = Path(zpath(str((dir_name / "ICOHPLIST.lobster").as_posix())))
icobilist_path = Path(zpath(str((dir_name / "ICOBILIST.lobster").as_posix())))
icooplist_path = Path(zpath(str((dir_name / "ICOOPLIST.lobster").as_posix())))

# Update lobsterpy analysis parameters with user supplied parameters
lobsterpy_kwargs_updated = {
Expand Down Expand Up @@ -563,24 +563,24 @@ def from_directory(
"""
dir_name = Path(dir_name)
calc_quality_kwargs = calc_quality_kwargs or {}
band_overlaps_path = Path(zpath(dir_name / "bandOverlaps.lobster"))
charge_path = Path(zpath(dir_name / "CHARGE.lobster"))
band_overlaps_path = Path(
zpath(str((dir_name / "bandOverlaps.lobster").as_posix()))
)
charge_path = Path(zpath(str((dir_name / "CHARGE.lobster").as_posix())))
doscar_path = Path(
zpath(
dir_name / "DOSCAR.LSO.lobster"
if Path(zpath(dir_name / "DOSCAR.LSO.lobster")).exists()
else Path(zpath(dir_name / "DOSCAR.lobster"))
)
zpath(str((dir_name / "DOSCAR.LSO.lobster").as_posix()))
if Path(zpath(str((dir_name / "DOSCAR.LSO.lobster").as_posix()))).exists()
else Path(zpath(str((dir_name / "DOSCAR.lobster").as_posix())))
)
lobsterin_path = Path(zpath(dir_name / "lobsterin"))
lobsterout_path = Path(zpath(dir_name / "lobsterout"))
lobsterin_path = Path(zpath(str((dir_name / "lobsterin").as_posix())))
lobsterout_path = Path(zpath(str((dir_name / "lobsterout").as_posix())))
potcar_path = (
Path(zpath(dir_name / "POTCAR"))
if Path(zpath(dir_name / "POTCAR")).exists()
Path(zpath(str((dir_name / "POTCAR").as_posix())))
if Path(zpath(str((dir_name / "POTCAR").as_posix()))).exists()
else None
)
structure_path = Path(zpath(dir_name / "POSCAR"))
vasprun_path = Path(zpath(dir_name / "vasprun.xml"))
structure_path = Path(zpath(str((dir_name / "POSCAR").as_posix())))
vasprun_path = Path(zpath(str((dir_name / "vasprun.xml").as_posix())))

# Update calc quality kwargs supplied by user
calc_quality_kwargs_updated = {
Expand Down Expand Up @@ -722,7 +722,7 @@ class LobsterTaskDocument(StructureMetadata, extra="allow"): # type: ignore[cal
None, description="pymatgen Icohplist object with ICOBI data"
)

schema: str = Field(
atomate2_version: str = Field(
__version__, description="Version of atomate2 used to create the document"
)

Expand Down Expand Up @@ -787,25 +787,35 @@ def from_directory(
dir_name = Path(dir_name)

# Read in lobsterout and lobsterin
lobsterout_doc = Lobsterout(Path(zpath(dir_name / "lobsterout"))).get_doc()
lobsterout_doc = Lobsterout(
Path(zpath(str((dir_name / "lobsterout").as_posix())))
).get_doc()
lobster_out = LobsteroutModel(**lobsterout_doc)
lobster_in = LobsterinModel(
**Lobsterin.from_file(Path(zpath(dir_name / "lobsterin")))
**Lobsterin.from_file(Path(zpath(str((dir_name / "lobsterin").as_posix()))))
)

icohplist_path = Path(zpath(dir_name / "ICOHPLIST.lobster"))
icooplist_path = Path(zpath(dir_name / "ICOOPLIST.lobster"))
icobilist_path = Path(zpath(dir_name / "ICOBILIST.lobster"))
cohpcar_path = Path(zpath(dir_name / "COHPCAR.lobster"))
charge_path = Path(zpath(dir_name / "CHARGE.lobster"))
cobicar_path = Path(zpath(dir_name / "COBICAR.lobster"))
coopcar_path = Path(zpath(dir_name / "COOPCAR.lobster"))
doscar_path = Path(zpath(dir_name / "DOSCAR.lobster"))
structure_path = Path(zpath(dir_name / "POSCAR"))
madelung_energies_path = Path(zpath(dir_name / "MadelungEnergies.lobster"))
site_potentials_path = Path(zpath(dir_name / "SitePotentials.lobster"))
gross_populations_path = Path(zpath(dir_name / "GROSSPOP.lobster"))
band_overlaps_path = Path(zpath(dir_name / "bandOverlaps.lobster"))
icohplist_path = Path(zpath(str((dir_name / "ICOHPLIST.lobster").as_posix())))
icooplist_path = Path(zpath(str((dir_name / "ICOOPLIST.lobster").as_posix())))
icobilist_path = Path(zpath(str((dir_name / "ICOBILIST.lobster").as_posix())))
cohpcar_path = Path(zpath(str((dir_name / "COHPCAR.lobster").as_posix())))
charge_path = Path(zpath(str((dir_name / "CHARGE.lobster").as_posix())))
cobicar_path = Path(zpath(str((dir_name / "COBICAR.lobster").as_posix())))
coopcar_path = Path(zpath(str((dir_name / "COOPCAR.lobster").as_posix())))
doscar_path = Path(zpath(str((dir_name / "DOSCAR.lobster").as_posix())))
structure_path = Path(zpath(str((dir_name / "POSCAR").as_posix())))
madelung_energies_path = Path(
zpath(str((dir_name / "MadelungEnergies.lobster").as_posix()))
)
site_potentials_path = Path(
zpath(str((dir_name / "SitePotentials.lobster").as_posix()))
)
gross_populations_path = Path(
zpath(str((dir_name / "GROSSPOP.lobster").as_posix()))
)
band_overlaps_path = Path(
zpath(str((dir_name / "bandOverlaps.lobster").as_posix()))
)

icohp_list = icoop_list = icobi_list = None
if icohplist_path.exists():
Expand Down Expand Up @@ -879,7 +889,7 @@ def from_directory(

# Read in LSO DOS
lso_dos = None
doscar_lso_path = Path(zpath(dir_name / "DOSCAR.LSO.lobster"))
doscar_lso_path = Path(zpath(str((dir_name / "DOSCAR.LSO.lobster").as_posix())))
if store_lso_dos and doscar_lso_path.exists():
doscar_lso_lobster = Doscar(
doscar=doscar_lso_path, structure_file=structure_path
Expand Down
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